def testBuildCifFromOE(self):
"""Build chemical component definitions from OE Mol object"""
try:
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory()
#
for ccId, ccObj in list(ccMolD.items())[:10]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
ok = oemf.build(molBuildType="model-xyz")
self.assertTrue(ok)
fp = os.path.join(self.__ccCifPath, ccId + "-gen.cif")
oeMol = oemf.getMol()
oeccU = OeChemCompUtils()
ok = oeccU.addOeMol(ccId,
oeMol,
missingModelXyz=False,
writeIdealXyz=False)
self.assertTrue(ok)
ok = oeccU.write(fp)
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __buildChemCompSearchIndex(self, ccObjD, descrD, limitPerceptions=False, molLimit=None):
"""Internal method return a dictionary of extracted chemical component descriptors and formula."""
rD = {}
try:
for ii, ccId in enumerate(ccObjD, 1):
if molLimit and ii > molLimit:
break
# ----
oemf = OeMoleculeFactory()
oemf.setQuiet()
tId = oemf.setChemCompDef(ccObjD[ccId])
if tId != ccId:
logger.error("%s chemical component definition import error", ccId)
# ----
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi, "chemaxon-smiles")
# ----
smiD = oemf.buildRelated(limitPerceptions=limitPerceptions)
logger.debug("%s related molecular forms %d", ccId, len(smiD))
rD.update(smiD)
except Exception as e:
logger.exception("Failing with %s", str(e))
return rD
def __buildChemCompSearchIndex(self, procName, ccIdList, descrD, limitPerceptions=False, quietFlag=False):
"""Internal method return a dictionary of extracted chemical component descriptors and formula."""
rL = []
fL = []
try:
for ccId in ccIdList:
if ccId not in self.__ccObjD:
logger.error("%s missing chemical definition for %s", procName, ccId)
fL.append(ccId)
continue
dataContainer = self.__ccObjD[ccId]
# ----
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
tId = oemf.setChemCompDef(dataContainer)
if tId != ccId:
logger.error("%s %s chemical component definition import error", procName, ccId)
fL.append(ccId)
continue
# ----
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi, "chemaxon-smiles")
# ----
relD = oemf.buildRelated(limitPerceptions=limitPerceptions)
logger.debug("%s %s related molecular forms %d", procName, ccId, len(relD))
if relD:
rL.extend([relD[v] for v in relD])
else:
fL.append(ccId)
except Exception as e:
logger.exception("%s failing with %s", procName, str(e))
return rL, fL
def testRoundTripOps(self):
"""Test IO operation on generated related molecules"""
try:
oeIoU = OeIoUtils()
mU = MarshalUtil()
mU.mkdir(self.__molfileDirPath)
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory()
for ccId, ccObj in list(ccMolD.items())[:10]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
relatedIdxD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s generated %d molecular forms", ccId,
len(relatedIdxD))
for sId, idxD in relatedIdxD.items():
logger.info("sId %r smiles %r", sId, idxD["smiles"])
mol2Path = os.path.join(self.__molfileDirPath,
sId + ".mol2")
oeMol = oeIoU.descriptorToMol(idxD["smiles"],
"oe-iso-smiles",
limitPerceptions=False,
messageTag=None)
oeIoU.write(mol2Path,
oeMol,
constantMol=True,
addSdTags=True)
tMolL = oeIoU.fileToMols(mol2Path)
#
nextMol2Path = os.path.join(self.__molfileDirPath,
sId + "-next.mol2")
oeIoU.write(nextMol2Path,
tMolL[0],
constantMol=True,
addSdTags=True)
sdfPath = os.path.join(self.__molfileDirPath, sId + ".mol")
oeMol = oeIoU.descriptorToMol(idxD["smiles"],
"oe-iso-smiles",
limitPerceptions=False,
messageTag=None)
oeIoU.write(sdfPath,
oeMol,
constantMol=True,
addSdTags=True)
#
tMolL = oeIoU.fileToMols(sdfPath)
nextSdfPath = os.path.join(self.__molfileDirPath,
sId + "-next.sdf")
oeIoU.write(nextSdfPath,
tMolL[0],
constantMol=True,
addSdTags=True)
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testBuildRelated(self):
"""Test build molecules chemical definitions -"""
try:
logger.info("Starting")
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory(quietMode=True)
relD = {}
for ccId, ccObj in list(ccMolD.items())[:100]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
tD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s related molecular forms %d", ccId, len(tD))
relD.update(tD)
logger.info("Total molecular forms (%d)", len(relD))
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def stringToMols(self, txt, sType="mol2", use3D=False):
"""Parse the input string as input format type (sType) returning a list of
molecule objects (OeGraphMol)
Args:
txt (str): string text of molecule data
sType (str, optional): string data format (mol2, sdf, smiles) . Defaults to "mol2".
Returns:
list: list of OeGraphMol() objects
"""
#
mL = []
oemf = OeMoleculeFactory()
try:
if sType not in ["mol2", "sdf", "smiles"]:
logger.error("Unsupported string data format")
return None
fD = {
"mol2": oechem.OEFormat_MOL2,
"sdf": oechem.OEFormat_SDF,
"smiles": oechem.OEFormat_SMI
}
ifs = oechem.oemolistream()
ifs.SetFormat(fD["sType"])
if not ifs.openstring(txt):
logger.error("Unable open string data for molecule reader")
return None
for tMol in ifs.GetOEGraphMols():
oeMol = oechem.OEGraphMol(tMol)
if use3D:
mL.append(
oemf.updateOePerceptions3D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
else:
mL.append(
oemf.updateOePerceptions2D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
except Exception as e:
logger.exception("Failing with %s", str(e))
return mL
def testDepictByBuildType(self):
"""Compare depictions constructed molecules with various builds from chemical defintions -"""
try:
ccIdList = self.__ccIdList
ccMolD = self.__getChemCompDefs()
#
limitPerceptions = True
molBuildTypeL = ["model-xyz", "ideal-xyz", "connection-table", "oe-iso-smiles"]
#
startTime = time.time()
oefm = OeMoleculeFactory()
for molBuildType in molBuildTypeL:
for ccId in ccIdList:
ccObj = ccMolD[ccId]
# ----
tId = oefm.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
ok = oefm.build(molBuildType=molBuildType, limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s", molBuildType, ccId)
continue
#
oeMol = oefm.getGraphMol()
pS = "-limited" if limitPerceptions else ""
imagePath = os.path.join(self.__workPath, ccId + "-%s%s.svg" % (molBuildType, pS))
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=False, labelAtomCIPStereo=True, labelAtomIndex=False, labelBondIndex=False, cellBorders=False, bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
logger.info("Completed depictions on %d molecules (%.4f seconds)", len(ccIdList) * len(molBuildTypeL), time.time() - startTime)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def fileToMols(self, filePath, use3D=False, largestPart=False):
"""Parse the input path returning a list of molecule objects (OeGraphMol).
Args:
filePath (str): file path must have strandard recognized extension ('mol', 'sdf', 'smi', 'oeb').
Returns:
list : list of OeGraphMol() objects
"""
mL = []
oemf = OeMoleculeFactory()
try:
ifs = oechem.oemolistream()
if ifs.open(filePath):
for tMol in ifs.GetOEGraphMols():
oeMol = oechem.OEGraphMol(tMol)
# if oechem.OEReadMolecule(ifs, oeMol):
if largestPart:
molL = oemf.getParts(oeMol)
if len(molL) > 0:
oeMol = molL[0]
logger.info(
"Using largest bonded molecule part (%d/%d)",
len(molL), oeMol.NumAtoms())
if use3D:
mL.append(
oemf.updateOePerceptions3D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
else:
mL.append(
oemf.updateOePerceptions2D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
except Exception as e:
logger.exception("Failing with %s", str(e))
return mL
def prefilterIndex(self,
oeQueryMol,
idxP,
matchOpts="relaxed",
skipFeatures=False):
"""Filter the full search index base on minimum chemical formula an feature criteria.
Args:
oeQueryMol (object): search target moleculed (OEMol)
idxP (object): instance ChemCompSearchIndexProvider()
matchOpts (str, optional): search criteria options. Defaults to "default".
skipFeatures (bool, optional): skip feature filters. Defaults to False.
Returns:
(list): list of chemical component identifiers in the filtered search space
"""
startTime = time.time()
oemf = OeMoleculeFactory()
oemf.setOeMol(oeQueryMol, "queryTarget")
typeCountD = oemf.getElementCounts(useSymbol=True)
# ccIdL1 = idxP.filterMinimumMolecularFormula(typeCountD)
#
featureCountD = oemf.getFeatureCounts() if not skipFeatures else {}
# Adjust filter according to search options
if matchOpts in matchOpts in [
"relaxed", "graph-relaxed", "simple",
"sub-struct-graph-relaxed"
]:
for ky in ["rings_ar", "at_ar", "at_ch"]:
featureCountD.pop(ky, None)
elif matchOpts in [
"relaxed-stereo", "graph-relaxed-stereo",
"sub-struct-graph-relaxed-stereo", "graph-relaxed-stereo-sdeq",
"sub-struct-graph-relaxed-stereo-sdeq"
]:
for ky in ["rings_ar", "at_ar"]:
featureCountD.pop(ky, None)
elif matchOpts in [
"default", "strict", "graph-strict", "graph-default",
"sub-struct-graph-strict"
]:
pass
ccIdL = idxP.filterMinimumFormulaAndFeatures(typeCountD, featureCountD)
logger.info(
"Pre-filtering results for formula+feature %d (%.4f seconds)",
len(ccIdL),
time.time() - startTime)
return ccIdL
def write(self, filePath, oeMol, constantMol=False, addSdTags=True):
"""Write an oeMol with format type inferred from the filePath extension (e.g. .mol)
Args:
filePath (str): filepath with a chemical type extension
constantMol (bool, optional): copies molecule before performing format specific perceptions
Returns:
bool: True for success or False otherwise
"""
try:
molId = os.path.splitext(os.path.basename(filePath))[0]
fmt = os.path.splitext(os.path.basename(filePath))[1][1:].lower()
#
if addSdTags:
oemf = OeMoleculeFactory()
oemf.setOeMol(oeMol, molId)
oemf.addSdTags()
oeMol = oemf.getMol()
#
self.__mU.mkdir(os.path.dirname(filePath))
ofs = oechem.oemolostream()
ofs.open(filePath)
logger.debug("Writing (fmt=%s) molId %s path %s title %s", fmt,
molId, filePath, oeMol.GetTitle())
#
if constantMol:
oechem.OEWriteConstMolecule(ofs, oeMol)
else:
oechem.OEWriteMolecule(ofs, oeMol)
#
# If this is a mol2 file, we need to replace the resname
if fmt.startswith("mol2"):
# If this is a mol2/mol2h substitute the default substructure id
with open(filePath, "r", encoding="utf-8") as ifh:
lines = ifh.readlines()
lines = [line.replace("<0>", molId) for line in lines]
with open(filePath, "w", encoding="utf-8") as ofh:
ofh.writelines(lines)
return True
except Exception as e:
logger.exception("Failing for %s with %s", filePath, str(e))
return False
def testBuildRelatedExtra(self):
"""Test build molecules chemical definitions including extra chemaxon descriptors"""
try:
caxP = ChemAxonDescriptorProvider(
ccUrlTarget=self.__ccUrlTarget,
birdUrlTarget=self.__birdUrlTarget,
cachePath=self.__cachePath,
useCache=True,
ccFileNamePrefix="cc-abbrev")
ok = caxP.testCache()
self.assertTrue(ok)
descrD = caxP.getDescriptorIndex()
#
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory(quietMode=True)
relD = {}
for ccId, ccObj in list(ccMolD.items())[:100]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
#
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi,
"chemaxon-smiles")
#
tD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s related molecular forms %d", ccId, len(tD))
relD.update(tD)
logger.info("Total molecular forms (%d)", len(relD))
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def chemCompToMol(self,
ccdFilePath,
molBuildType="model-xyz",
quietFlag=False):
retMolL = []
try:
rdCcObjL = self.__mU.doImport(ccdFilePath, fmt="mmcif")
logger.info("Read %s with %d definitions", ccdFilePath,
len(rdCcObjL))
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
for ccObj in rdCcObjL:
ccId = oemf.setChemCompDef(ccObj)
if ccId:
ok = oemf.build(molBuildType=molBuildType)
if ok:
oeMol = oemf.getMol()
retMolL.append(oeMol)
except Exception as e:
logger.exception("Loading %s failing with %s", ccdFilePath, str(e))
return retMolL
def testBuilders(self):
try:
ccMolD = self.__getChemCompDefs()
quietFlag = False
molBuildTypeL = ["model-xyz", "ideal-xyz"]
for molBuildType in molBuildTypeL:
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
#
eCount = 0
for tId, ccObj in ccMolD.items():
ccId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
logger.debug("Building %s using molBuildType %r", ccId,
molBuildType)
if ccId:
ok = oemf.build(molBuildType=molBuildType)
logger.debug(
"Comparing built component %s using molBuildType %r",
ccId, molBuildType)
# ok = oemf.compare()
ok = True
if not ok:
logger.info("Failing on %s molBuildType %r", ccId,
molBuildType)
eCount += 1
# self.assertTrue(ok)
else:
logger.error("Cannot process %r", ccObj.getName())
logger.info(
"Processed %d components molBuildType %r errors %d",
len(ccMolD), molBuildType, eCount)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def getCCDefFile(self, ccFilePath, molBuildType="model-xyz", suppressHydrogens=False):
"""Fetch the molecule definition (ccPath) and build OE molecules
for comparison.
"""
#
mU = MarshalUtil(workPath=self.__workPath)
rdCcObjL = mU.doImport(ccFilePath, fmt="mmcif")
oemf = OeMoleculeFactory()
if not self.__verbose:
oemf.setQuiet()
ccId = oemf.setChemCompDef(rdCcObjL[0])
oemf.build(molBuildType=molBuildType)
if self.__verbose:
logger.info(" CCId = %s", ccId)
logger.info(" Title = %s", oemf.getTitle())
logger.info(" SMILES = %s", oemf.getCanSMILES())
logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES())
logger.info(" Formula (Hill) = %s", oemf.getFormula())
logger.info(" InChI key = %s", oemf.getInChIKey())
logger.info(" InChI = %s", oemf.getInChI())
fD = {}
fD = {"Formula": oemf.getFormula(), "SMILES": oemf.getCanSMILES(), "SMILES_STEREO": oemf.getIsoSMILES(), "InChI": oemf.getInChI(), "InChIKey": oemf.getInChIKey()}
if suppressHydrogens:
tMol = oemf.getGraphMolSuppressH()
else:
tMol = oemf.getMol()
fD["OEMOL"] = tMol
fD["xyz"] = oemf.getAtomDetails(xyzType="model")
return (ccId, tMol, fD)
def testSssWithFingerPrintFromDescriptor(self):
oemp = OeMoleculeProvider(**self.__myKwargs)
ok = oemp.testCache()
ccmP = ChemCompIndexProvider(**self.__myKwargs)
ccIdxD = ccmP.getIndex()
ok = ccmP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
limitPerceptions = False
# minFpScore = 0.5
maxFpResults = 50
matchOpts = "graph-relaxed"
numMols = 20
oeioU = OeIoUtils()
oesU = OeSearchUtils(oemp, fpTypeList=self.__fpTypeList)
missTupL = []
missedD = {}
missedFpD = {}
# ----
startTime = time.time()
for ccId, ccD in list(ccIdxD.items())[:numMols]:
for buildType in [
"oe-iso-smiles", "oe-smiles", "acdlabs-smiles",
"cactvs-iso-smiles", "cactvs-smiles", "inchi"
]:
if buildType in ccD:
logger.debug("Search %s %r", ccId, ccD[buildType])
if buildType in ["inchi"]:
oemf = OeMoleculeFactory()
oemf.setDescriptor(ccD["inchi"], "inchi", ccId)
ok = oemf.build(molBuildType="inchi",
limitPerceptions=limitPerceptions)
if not ok:
logger.info("%s build failed with InChI %r", ccId,
ccD["inchi"])
else:
oeMol = oemf.getMol()
if oemf.getInChI() != ccD["inchi"]:
logger.info(
"%s regenerated InChI differs\n%r\n%s",
ccId, ccD["inchi"], oemf.getInChI())
else:
oeMol = oeioU.smilesToMol(
ccD[buildType], limitPerceptions=limitPerceptions)
if not oeMol:
continue
maxHits = 0
minHits = maxFpResults
selfHit = False
for fpType, minFpScore in self.__fpTypeCuttoffList:
retStatus, mL = oesU.searchSubStructureWithFingerPrint(
oeMol,
fpType,
minFpScore,
maxFpResults,
matchOpts=matchOpts)
self.assertTrue(retStatus)
logger.debug("%s fpType %r hits %d", ccId, fpType,
len(mL))
maxHits = max(maxHits, len(mL))
minHits = min(minHits, len(mL))
matchedSelf = self.__resultContains(ccId, mL)
selfHit = selfHit or matchedSelf
if not matchedSelf:
missedFpD.setdefault(ccId, []).append(
(buildType, fpType, len(mL)))
if not selfHit:
missedD.setdefault(ccId, []).append(buildType)
logger.info("%s (%r) buildType %r min hits %d max hits %d",
ccId, selfHit, buildType, minHits, maxHits)
else:
logger.info("%s missing descriptor %r", ccId, buildType)
#
for ccId, missL in missedD.items():
logger.info("%s missed list %r", ccId, missL)
if ccId in missedFpD:
logger.info("%s unmatched for fpTypes %r", ccId,
missedFpD[ccId])
# ----
doDepict = False
if doDepict:
mD = {}
for missTup in missTupL:
mD.setdefault(missTup[0], []).append(missTup[1])
for ccId, buildTypeL in mD.items():
idxD = ccIdxD[ccId]
if "oe-iso-smiles" in idxD:
for buildType in buildTypeL:
self.__displayAlignedDescriptorPair(
ccId,
idxD["oe-iso-smiles"],
"oe-iso-smiles",
idxD[buildType],
buildType,
title=None,
limitPerceptions=True)
logger.info("%s fingerprints search on %d in (%.4f seconds)",
len(self.__fpTypeList), numMols,
time.time() - startTime)
def __getMiscFile(self, filePath, suppressHydrogens=False, importType="2D", title=None, largestPart=False):
"""Fetch a miscellaneous chemical file (ccPath) and build OE molecules
for comparison.
"""
try:
oeioU = OeIoUtils()
oeMolL = oeioU.fileToMols(filePath, use3D=importType == "3D", largestPart=largestPart)
logger.info("Read (%d) from %s ", len(oeMolL), filePath)
oeMol = oeMolL[0]
ccId = title if title else oeMol.GetTitle()
if title:
oeMol.SetTitle(ccId)
#
oemf = OeMoleculeFactory()
if not self.__verbose:
oemf.setQuiet()
oemf.setOeMol(oeMol, ccId)
#
fD = oemf.getOeMoleculeFeatures()
if self.__verbose:
logger.info(" Title = %s", title)
logger.info(" Title OEMF = %s", oemf.getTitle())
logger.info(" SMILES = %s", oemf.getCanSMILES())
logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES())
logger.info(" Formula (Hill) = %s", oemf.getFormula())
logger.info(" InChI key = %s", oemf.getInChIKey())
logger.info(" InChI = %s", oemf.getInChI())
#
ccId = oemf.getTitle()
if suppressHydrogens:
tMol = oemf.getGraphMolSuppressH()
else:
tMol = oemf.getMol()
molXyzL = []
if importType == "3D":
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
molXyzL.append(
ComponentAtomDetails(
atIdx=atm.GetIdx(),
atNo=atm.GetAtomicNum(),
atName=atm.GetName(),
atType=atm.GetType(),
x=xyzL[0],
y=xyzL[1],
z=xyzL[2],
atFormalCharge=atm.GetFormalCharge(),
)
)
fD = {}
fD = {
"Formula": oemf.getFormula(),
"SMILES": oemf.getCanSMILES(),
"SMILES_STEREO": oemf.getIsoSMILES(),
"InChI": oemf.getInChI(),
"InChIKey": oemf.getInChIKey(),
"xyz": molXyzL,
}
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
if self.__verbose:
logger.debug("atom %s %s %s %s %r", atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(), atm.GetType(), xyzL)
fD["OEMOL"] = tMol
return (ccId, tMol, fD)
except Exception as e:
logger.exception("Failing with %s", str(e))
return None, None, None
def buildOeBinaryMolCache(self,
filePath,
ccObjD,
molBuildType="model-xyz",
quietFlag=False,
fpTypeList=None,
limitPerceptions=False,
suppressHydrogens=False):
"""Build cache of OEMol() objects from the input chemical component definition list.
Args:
filePath (str): output cache file path
ccObjD (dict): chemical component object dictionary
molBuildType (str, optional): [description]. Defaults to "model-xyz".
quietFlag (bool, optional): [description]. Defaults to False.
fpTypeList (list, optional): fingerprint type list. Defaults to None.
limitPerceptions (bool, optional): suppress automatic chemical perceptions. Defaults to False.
suppressHydrogens (bool, optional): suppress explicit hydrogen count. Defaults to False.
Returns:
(int, int, list): chem comp success count, error count, chem comp identifier failure list
"""
ok = False
startTime = time.time()
failIdList = []
ccCount = 0
errCount = 0
try:
ofs = oechem.oemolostream()
ofs.SetFormat(oechem.OEFormat_OEB)
if ofs.open(filePath):
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
for ccId, ccObj in ccObjD.items():
tId = oemf.setChemCompDef(ccObj)
if tId and tId == ccId:
ok = oemf.build(molBuildType=molBuildType,
limitPerceptions=limitPerceptions)
if ok and fpTypeList:
fpOk = oemf.addFingerPrints(fpTypeList)
if not fpOk:
logger.info(
"Fingerprint generation fails for %r",
ccId)
if ok:
oeMol = oemf.getMol(
suppressHydrogens=suppressHydrogens)
oechem.OEWriteMolecule(ofs, oeMol)
ccCount += 1
if not ok or not tId:
# build failed incomplete component (e.g. missing atoms or bonds)
errCount += 1
failIdList.append(ccId)
else:
logger.error("Unable to open cache database %s", filePath)
errCount += 1
except Exception as e:
logger.exception("Failing with %s", str(e))
#
endTime = time.time()
logger.info("Completed operation at %s (%.4f seconds)",
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - startTime)
return ccCount, errCount, failIdList
def buildOeBinaryMolCacheFromIndex(self,
filePath,
ccIdxD,
quietFlag=False,
fpTypeList=None,
limitPerceptions=False,
suppressHydrogens=False):
"""Build cache of OEGraphMol() objects from the input chemical component search index.
Args:
filePath (str): output cache file path
ccIdxD (dict): search index dictionary
quietFlag (bool, optional): suppress OE output. Defaults to False.
fpTypeList (list, optional): list of fingerprint types. Defaults to None.
limitPerceptions (bool, optional): suppress automatic chemical perceptions. Defaults to False.
suppressHydrogens (bool, optional): suppress explicit hydrogen count. Defaults to False.
Returns:
(int, int, list): chem comp success count, error count, chem comp identifier failure list
"""
failIdList = []
ccCount = 0
errCount = 0
startTime = time.time()
try:
ofs = oechem.oemolostream()
ofs.SetFormat(oechem.OEFormat_OEB)
if ofs.open(filePath):
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
for searchCcId, ccIdx in ccIdxD.items():
oemf.setDescriptor(ccIdx["smiles"], "oe-iso-smiles",
searchCcId)
ok = oemf.build(molBuildType="oe-iso-smiles",
limitPerceptions=limitPerceptions)
if ok and fpTypeList:
fpOk = oemf.addFingerPrints(fpTypeList)
if not fpOk:
logger.info("Fingerprint generation fails for %r",
searchCcId)
if ok:
if not suppressHydrogens:
oemf.addExplicitHydrogens()
oemf.setSimpleAtomNames()
oeMol = oemf.getMol(
suppressHydrogens=suppressHydrogens)
oechem.OEWriteMolecule(ofs, oeMol)
ccCount += 1
if not ok:
# build failed incomplete component (e.g. missing atoms or bonds)
errCount += 1
failIdList.append(searchCcId)
else:
logger.error("Unable to open cache database %s", filePath)
errCount += 1
except Exception as e:
logger.exception("Failing with %s", str(e))
#
endTime = time.time()
logger.info("Completed operation at %s (%.4f seconds)",
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - startTime)
return ccCount, errCount, failIdList
def testSelfConsistency(self):
"""Compare constructed molecule with underlying chemical definitions -"""
try:
failL = []
ccMolD = self.__getChemCompDefs()
#
# molBuildTypeL = ["model-xyz", "ideal-xyz", None]
# molBuildTypeL = [None]
#
oemf = OeMoleculeFactory()
macmp = MoleculeAnnotationsCompare()
limitPerceptions = False
# buildTypeRef = "oe-iso-smiles"
buildTypeRef = "model-xyz"
filterHydrogens = False
if buildTypeRef in [
"oe-iso-smiles", "oe-smiles", "cactvs-smiles",
"cactvs-iso-smiles", "acdlabs-smiles", "inchi"
]:
filterHydrogens = True
#
for ccId, ccObj in ccMolD.items():
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
ok = oemf.build(molBuildType=buildTypeRef,
limitPerceptions=limitPerceptions,
normalize=False)
if not ok:
logger.info("Build using %r failed for %s", buildTypeRef,
ccId)
continue
#
doTautomers = False
if doTautomers:
tautomerMolL = oemf.getTautomerMolList()
logger.info("%s number reasonable tautomers %d", ccId,
len(tautomerMolL))
#
refFD = macmp.getChemCompFeatures(
ccObj,
descriptorProgram="OPENEYE",
filterHydrogens=filterHydrogens)
tstFD = oemf.getOeMoleculeFeatures(
filterHydrogens=filterHydrogens)
# logger.info("tstFD %r", tstFD)
ok, retCmp = macmp.compare(refFD,
tstFD,
tstInfo="Openeye ISO SMILES")
if not ok:
logger.info("Comparison failed build type %r and %r",
buildTypeRef, ccId)
logger.debug(
"diff -> atomatic atoms %r stereo atoms %r bond types %r aromatic bonds %r",
retCmp.difAromaticAtoms,
retCmp.difStereoAtoms,
retCmp.difTypeBonds,
retCmp.difAromaticBonds,
)
failL.append(ccId)
#
logger.info("Failures (%d) %r: ", len(failL), failL)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __displayAlignedDescriptorPair(self,
ccId,
descrRef,
buildTypeRef,
descrFit,
buildTypeFit,
title=None,
limitPerceptions=True):
oemfRef = OeMoleculeFactory()
oemfRef.setDescriptor(descrRef, buildTypeRef, ccId)
oemfRef.build(molBuildType=buildTypeRef,
limitPerceptions=limitPerceptions)
oeMolRef = oemfRef.getMol()
#
oemfFit = OeMoleculeFactory()
oemfFit.setDescriptor(descrFit, buildTypeFit, ccId)
oemfFit.build(molBuildType=buildTypeFit,
limitPerceptions=limitPerceptions)
oeMolFit = oemfFit.getMol()
#
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType="graph-relaxed", minAtomMatchFraction=0.50)
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5)
oed.setRefMol(oeMolRef, ccId)
oed.setFitMol(oeMolFit, ccId)
myTitle = title if title else buildTypeRef + "-" + buildTypeFit
imgPath = os.path.join(self.__workPath, myTitle + "-" + ccId + ".svg")
logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
if aML:
logger.info("%s aligned image path %r", ccId, imgPath)
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
def testRoundTrip(self):
"""Round trip smiles comparisons -"""
try:
ccMolD = self.__getChemCompDefs()
# useCache = True
# quietFlag = False
# molBuildTypeL = ["model-xyz", "ideal-xyz", None]
# molBuildTypeL = [None]
buildTypeRef = "oe-iso-smiles"
oemf1 = OeMoleculeFactory()
oemf2 = OeMoleculeFactory()
#
for ccId, ccObj in ccMolD.items():
# ----
ccIt = iter(PdbxChemCompIt(ccObj))
cc = next(ccIt)
formula = cc.getFormulaWithCharge()
# ccId = cc.getId()
ccName = cc.getName()
ifCharge = cc.getFormalChargeAsInt()
isAmbiguous = cc.getAmbiguousFlag() in ["Y", "y"]
isCurrent = cc.getReleaseStatus() in ["REL"]
logger.debug("%s name %r formula %r charge %d", ccId, ccName,
formula, ifCharge)
# ----
ccId = oemf1.setChemCompDef(ccObj)
ok = oemf1.build(molBuildType=buildTypeRef,
limitPerceptions=False)
if not ok:
logger.info(
"Build using %r failed for %s (ambiguous flag %r current %r)",
buildTypeRef, ccId, isAmbiguous, isCurrent)
#
isDiff = False
#
if isDiff:
genIsoSmi = oemf1.getCanSMILES()
oemf2 = OeMoleculeFactory()
oemf2.setDescriptor(genIsoSmi, "oe-iso-smiles", ccId)
oemf2.build(molBuildType="oe-iso-smiles",
limitPerceptions=False)
regenIsoSmi = oemf2.getIsoSMILES()
if genIsoSmi != regenIsoSmi:
logger.info(
"%s regenerated ISOSMILES differ \n -- INP: %s\n -- OUT: %s",
ccId, genIsoSmi, regenIsoSmi)
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
highlightStyleFit="ballAndStickInverse",
highLightNotMatchColorRef="pink",
bondDisplayWidth=0.5,
)
oed.setRefMol(oemf1.getGraphMol(), ccId)
oed.setFitMol(oemf2.getGraphMol(), ccId)
imgPath = os.path.join(
self.__workPath,
"compare-assigned-" + ccId + "-calc-" + ccId + ".svg")
logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.info("%5s %-5s %5s %-5s", rCC, rAt, tCC,
tAt)
else:
logger.debug("%s matched all cases", ccId)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testCompareByBuildType(self):
"""Compare depictions constructed molecules with various builds from chemical defintions -
all build types 8769 (all)
connect - smiles 6743
model vs iso smiles 5937
ideal va iso smiles 7047
"""
doDepict = False
ccResultD = {}
genResultD = {}
smilesByBuildTypeD = {}
try:
ccMolD, ccIdxD = self.__getChemCompDefs()
#
limitPerceptions = True
# molBuildTypeL = ["model-xyz", "ideal-xyz", "connection-table", "oe-iso-smiles"]
molBuildTypeL = ["ideal-xyz", "oe-iso-smiles"]
#
startTime = time.time()
oefm = OeMoleculeFactory()
oefm.setQuiet()
for molBuildType in molBuildTypeL:
for ccId, idxD in ccIdxD.items():
ccObj = ccMolD[ccId]
# ----
ccIsoSmiles = idxD["oe-iso-smiles"]
ccSmiles = idxD["oe-smiles"]
# ----
tId = oefm.setChemCompDef(ccObj)
if not tId:
logger.info("Skipping bad component %r", ccId)
continue
self.assertEqual(tId, ccId)
ok = oefm.build(molBuildType=molBuildType,
limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s",
molBuildType, ccId)
continue
# ------
oeMol = oefm.getGraphMol()
oeIsoSmiles = oefm.getIsoSMILES()
oeSmiles = oefm.getCanSMILES()
ccEq = oeIsoSmiles == ccIsoSmiles and oeSmiles == ccSmiles
#
oefmR = OeMoleculeFactory()
oefmR.setQuiet()
ccIdGen = ccId + "_gen"
oefmR.setDescriptor(oeIsoSmiles, "oe-iso-smiles", ccIdGen)
ok = oefmR.build(molBuildType="oe-iso-smiles",
limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s",
molBuildType, ccIdGen)
continue
# ------
#
# oeMolGen = oefmR.getGraphMol()
oeIsoSmilesGen = oefmR.getIsoSMILES()
oeSmilesGen = oefmR.getCanSMILES()
genEq = oeIsoSmiles == oeIsoSmilesGen and oeSmiles == oeSmilesGen
smilesByBuildTypeD.setdefault(ccId, {}).setdefault(
molBuildType, []).append(oeIsoSmilesGen)
#
logger.debug("%s buildType %s ccEq %r genEq %r", ccId,
molBuildType, ccEq, genEq)
if not ccEq:
ccResultD.setdefault(molBuildType, []).append(ccId)
if not genEq:
genResultD.setdefault(molBuildType, []).append(ccId)
if doDepict:
pS = "-limited" if limitPerceptions else ""
imagePath = os.path.join(
self.__workPath,
ccId + "-%s%s.svg" % (molBuildType, pS))
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
cellBorders=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
logger.info(
"Completed comparing %d molecules in %d builds (%.4f seconds)",
len(ccIdxD), len(molBuildTypeL),
time.time() - startTime)
#
#
for molBuildType in molBuildTypeL:
if molBuildType in genResultD:
logger.info("GEN %s (%d) %r", molBuildType,
len(genResultD[molBuildType]),
genResultD[molBuildType])
numDiff = 0
for ccId, btD in smilesByBuildTypeD.items():
tS = set()
for molBuildType, sL in btD.items():
tS.add(sL[0])
if len(tS) > 1:
numDiff += 1
logger.debug("%s diff smiles (%d) %r", ccId, len(tS), tS)
logger.info("Components with inconsistent SMILES %d", numDiff)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __testReproduceDescriptors(self, molBuildType, limitPerceptions=True):
#
ccMolD, ccIdxD = self.__getChemCompDefs()
oemf = OeMoleculeFactory()
countD = defaultdict(int)
for ccId, ccDef in ccMolD.items():
tId = oemf.setChemCompDef(ccDef)
if ccId != tId:
continue
oemf.build(molBuildType=molBuildType,
limitPerceptions=limitPerceptions)
oeMol = oemf.getMol()
#
countD["total components"] += 1
if ccId not in ccIdxD:
logger.info("Missing ccIndex entry for %s", ccId)
continue
ccdD = ccIdxD[ccId]
if ccdD["ambiguous"]:
countD["ambiguous component"] += 1
continue
#
countD["total molecules"] += 1
nativeCanIsoSmiles = oechem.OECreateIsoSmiString(oeMol)
canIsoSmiles = oechem.OEMolToSmiles(oeMol)
isoSmiles = oemf.getIsoSMILES()
canSmiles = oemf.getCanSMILES()
# check interal consistency
if nativeCanIsoSmiles != isoSmiles:
logger.error("%s stored and calculated OE smiles differ %s %s",
ccId, nativeCanIsoSmiles, isoSmiles)
if canIsoSmiles != isoSmiles:
logger.error(
"%s calculated OE ISO and canonical smiles differ %s %s",
ccId, isoSmiles, canIsoSmiles)
# compare with archived values
if isoSmiles != ccdD["oe-iso-smiles"]:
logger.info("%s ISO SMILES differ \nccd: %r \nOE: %r", ccId,
ccdD["oe-iso-smiles"], isoSmiles)
countD["iso_smiles_diff"] += 1
# ----------
if canSmiles != ccdD["oe-smiles"]:
logger.info("%s CAN SMILES differ \nccd: %r \nOE: %r", ccId,
ccdD["oe-smiles"], canSmiles)
countD["smiles_diff"] += 1
formula = oemf.getFormula()
if formula.upper() != ccdD["formula"].upper():
logger.debug("%s formulas differ \nccd: %r \nOE: %r", ccId,
ccdD["formula"], formula)
countD["formula_diff"] += 1
# ---------
inchiKey = oemf.getInChIKey()
if inchiKey != ccdD["inchikey"]:
logger.debug("%s InChI keys differ \nccd: %r \nOE: %r", ccId,
ccdD["inchikey"], inchiKey)
countD["inchikey_diff"] += 1
#
inchi = oemf.getInChI()
if inchi != ccdD["inchi"]:
logger.debug("%s InChIs differ \nccd: %r \nOE: %r", ccId,
ccdD["inchi"], inchi)
countD["inchi_diff"] += 1
#
#
for ky, vl in countD.items():
logger.info("%-12s %6d", ky, vl)
def __buildChemCompIndex(self,
cD,
molBuildType="model-xyz",
doFeatures=True):
"""Internal method return a dictionary of extracted chemical component descriptors and formula."""
rD = {}
try:
quietFlag = True
for _, dataContainer in cD.items():
ccIt = iter(PdbxChemCompIt(dataContainer))
cc = next(ccIt, None)
ccId = cc.getId()
formula = str(cc.getFormula()).replace(" ", "")
ambiguousFlag = cc.getAmbiguousFlag().upper() in ["Y", "YES"]
tch = cc.getFormalCharge()
fcharge = int(tch) if tch and tch not in [".", "?"] else 0
#
logger.debug("ccId %r formula %r ambiguous %r fcharge %r",
ccId, formula, ambiguousFlag, fcharge)
if fcharge:
sign = "+" if fcharge > 0 else "-"
mag = str(abs(fcharge)) if abs(fcharge) > 1 else ""
formula = formula + sign + mag
#
atIt = PdbxChemCompAtomIt(dataContainer)
typeCounts = defaultdict(int)
for at in atIt:
aType = at.getType().upper()
typeCounts[aType] += 1
#
rD[ccId] = {
"formula": formula,
"type-counts": typeCounts,
"ambiguous": ambiguousFlag,
"feature-counts": {}
}
desIt = PdbxChemCompDescriptorIt(dataContainer)
for des in desIt:
desBuildType = des.getMolBuildType()
tS = des.getDescriptor()
descr = tS.strip() if tS else None
if not descr:
continue
if desBuildType in [
"oe-iso-smiles", "oe-smiles", "acdlabs-smiles",
"cactvs-iso-smiles", "cactvs-smiles", "inchi",
"inchikey"
]:
rD[ccId][desBuildType] = descr
else:
logger.error("%s unexpected descriptor build type %r",
ccId, desBuildType)
if doFeatures:
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
tId = oemf.setChemCompDef(dataContainer)
if tId != ccId:
logger.error(
"%s chemical component definition import error",
ccId)
continue
ok = oemf.build(molBuildType=molBuildType)
if ok:
rD[ccId]["feature-counts"] = oemf.getFeatureCounts()
except Exception as e:
logger.exception("Failing with %s", str(e))
return rD
def getCCDefObj(self, dataContainer, molBuildType="model-xyz", suppressHydrogens=False):
"""Build OE molecule from the input chemical component definition object."""
#
oemf = OeMoleculeFactory()
if not self.__verbose:
oemf.setQuiet()
ccId = oemf.setChemCompDef(dataContainer)
oemf.build(molBuildType=molBuildType)
if self.__verbose:
logger.info(" CCId = %s", ccId)
logger.info(" Title = %s", oemf.getTitle())
logger.info(" SMILES = %s", oemf.getCanSMILES())
logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES())
logger.info(" Formula (Hill) = %s", oemf.getFormula())
logger.info(" InChI key = %s", oemf.getInChIKey())
logger.info(" InChI = %s", oemf.getInChI())
fD = {}
fD = {"Formula": oemf.getFormula(), "SMILES": oemf.getCanSMILES(), "SMILES_STEREO": oemf.getIsoSMILES(), "InChI": oemf.getInChI(), "InChIKey": oemf.getInChIKey()}
if suppressHydrogens:
tMol = oemf.getGraphMolSuppressH()
else:
tMol = oemf.getMol()
fD["OEMOL"] = tMol
fD["xyz"] = oemf.getAtomDetails(xyzType="model")
return (ccId, tMol, fD)